Alistair, who pushed Jonny over the line ahead of him in second, said the condition his brother was in was "as close to death as you can be in sport" had he not received immediate medical attention at the finish line.
Jonny went into the final race of the season in Cozumel, Mexico, in second place in the standings behind Spaniard Mario Mola, with Olympic champion Alistair out of contention having missed earlier races.
Rio silver winner Jonny needed to win the race and for Mola to finish no higher than fourth, and that was exactly what looked set to happen after the brothers had again pushed the pace hard on the swim and bike legs.
South African Henri Schoeman, who won bronze behind the Brownlees in Rio, overtook Jonny to win the race.
Jonny second-place step on the podium was left empty while Alistair and Mola heard the Spanish anthem but World Triathlon said this was a precaution.
"Following the race [Jonny Brownlee] was in recovery and doing a lot better," they said on Twitter. "But just for safety precautions he was sent to the hospital."